How would I have made ME more interesting?
1) I wouldn't have lifted the main plot from Star Control 3: Every aeon, an inscrutable alien intelligence returns to the galaxy to wipe it of sentient life. The last time these Eternal Ones/Reapers came, they wiped out the Precursors/Protheans, who left ruins and artifacts scattered over the galaxy, which remain a mystery to all current spacefaring races, due to their rarity and advanced technology. You play the commander of the most advanced ship in the human fleet, whose job it is to discover the threat, and figure out how to avert the coming catastrophe.
2) I'd have created a more interesting science fiction universe, one that includes/extrapolates on some of the scientific discoveries we've made in the past, oh, 30 years.
2a) The Normandy, as a stealth ship, would have included the metamaterials we invented years ago, as well as the ability to use waste heat to generate power. This would have solved both the problems with the ship as stated in the game - respectively, the inability to hide from visual sensors, and the need for the ship to eventually stop running "silent" and vent tons of waste heat before it cooks everyone in the ship.
Metamaterials:
http://www.gizmag.com/go/7186/
http://www.gizmag.com/metamaterials-invisible-ships/8906/
Heat to Electrical Energy:
http://www.gizmag.com/energy-efficiency-breakthroughs-at-mit-and-berkeley/8790/
2b) None of the current nanotech and biotech breakthroughs are represented in ME, never mind a logical extrapolation of where they'd be almost 300 years from now, with the exception of a small, pointless side-quest that mentions in-vitro treatment of a genetic disorder (that's amazingly still considered unreliable).
Seeing as it would be impossible for a squad of baseline humans to take on a single true-AI death machine in open combat with small arms (never mind plow through dozens of AI opponents as if they were goblins), Shepard and his military cohorts should all have been bio- and nanotech-enhanced posthumans, which would be the only thing that could conceivably put them on equal footing with their opponents.
The Geth, as full AI wardroids, should have been -terrifying- opponents, and it should have been hammered home that an unenhanced organic could in no way stand up to them, short of dropping nukes on them, or throwing waves at them, at a 100+ to 1 ratio.
Of course, military-grade enhancements would be far more than the average citizen would be equipped with. Your average citizen would probably only have life-extension/health related enhancements, plus whatever they'd need to excel in their chosen careers. And there may be religious communities of baseline humans that refuse any technology that extends their lifespans at all. This would make for a more interesting society as any or all of these segments of human culture come into conflict, and if true AI are banned, there'd be a concern that the highest level of posthuman may start blurring the line between organic and artificial intelligence. Shepard and crew might start questioning their own humanity, as the distance between themselves and baseline humans gets wider and wider.
This would makes for a much more compelling future human culture and deeper writing opportunities would abound.
2c) Take Joker out of the cockpit, and remove his genetic condition that would have been cured a century or two before. The idea of manually-piloted spaceships is beyond ridiculous anyway.
3) I'd have kept magic (psychic powers) out of the setting, and differentiated my game world even more from every other ultra-soft sci-fi game out there. Even if it wouldn't be diamond-hard science fiction, it'd still be harder than most.
4) I'd have come up with another reason why organics like Saren would help the Reapers other than mind-control powers. The game pretends Saren is rational, or at least perceives himself as rational, until you get to the end, and you yell at him "The Reaper's lying! Kill yourself!" and he fights off the brainwashing long enough to go "You're right! BANG".
5) This may be solved in the sequels, but it seems to me that Bioware's written itself into the corner with the Reapers. Their goals and methods and low levels of technology make no sense, from what we've seen so far. Beings that have been around as long as they have would not have any problem facing down primitives like us. The fact that one ship of something 50,000 years more advanced (at minimum, and that's only if they were lying about the Protheans not having been their first victims) than the next ship in the area was defeated by that fleet at the end is less likely than a modern battleship being defeated by the Spanish Armada, and that's only a technology difference of about 500 years
Also, the way to wipe out all sentient life in the galaxy is to seed it with self-replicating
Von Neumann probes, especially if those probes also seed every planet they come across with nanites that disassemble any form of life above a certain level of complexity. Perfect hands-off, no-effort galactic sterility.
So, the question is - why do the Reapers have such lousy technology considering how long they've been around, and why do they take such an inefficient, convoluted, and ultimately ineffective route to accomplishing their supposed goal, akin to drinking a glass of water by constructing a Rube Goldberg device every time you get thirsty, as opposed to simply picking up the glass with your damn hand?
6) Consequences other than the gaining of Renegade/Paragon points, though this may be fixed in the sequels, if they read saves and implement consequences for choices made in the first chapter.
7) Less, but more interesting combat, which includes better teammate and enemy AI. Even at the hardest difficulty, I found combat incredibly easy, but incredibly boring, because I was the only person on the battlefield that wasn't retarded. I ended up turning the difficulty down to low just to make combat end quicker.
8) No minigames.
9) No armor/weapon collection. At the highest echelons of military special operations, soldiers do not have to scavenge/purchase all their own equipment. The government is generally happy to provide that.
10) Better exploration. Why does everything have anti-grav propulsion except the Mako? Why is every world heavily mountainous, only gray, green, red, brown, or white? Also, a reason to explore that doesn't make me feel like a complete tool for utterly ignoring the impending death of all sentient life so I can go rock climbing in my space truck.
I guess that's about it off the top of my head. Keep in mind that a lot of this is subjective taste, and what may have made the game much more interesting to me wouldn't have mattered, or even may have made it less interesting, to others.